Recovery Successful But...

Hello,
... I am having a little annoying issue.

My laptops hard drive has been destroyed by rain. Luckily I have ATI! I ordered a new (bigger HD) to recover my info. I booted from the recovery disk and I chose the entire disc (including MBR). I don't know how long the recovery actually took because I left it while it ran. When I got home it said it was successful. So, I restarted my machine and it said that it couldn't find the MBRBoot file (I'm not exactly sure what it is called). So that was problem one. I popped in my Windows 7 disc and it repaired it - and it worked! When Windows was up and running it went really slow, but then performance picked up over time.

Now, since then I have noticed all my software installations were really slow. No matter how small the install file is. I was updating JungleDisk (and online backup) which is a small file and the updates usually complete in less than a minute. This update took about 10-15 minutes. Right now, I had just uninstalled Microsoft Office 2010 and that took about twenty minutes. I don't know why they are taking so long. Before these installations, I ran CCleaner to try and fix registry errors, but I guess it didn't help.

What can I do?

Thanks!